microRNA-31 regulates skeletogenesis by direct suppression of Eve and Wnt1

Dev Biol. 2021 Apr:472:98-114. doi: 10.1016/j.ydbio.2021.01.008. Epub 2021 Jan 20.


microRNAs (miRNAs) play a critical role in a variety of biological processes, including embryogenesis and the physiological functions of cells. Evolutionarily conserved microRNA-31 (miR-31) has been found to be involved in cancer, bone formation, and lymphatic development. We previously discovered that, in the sea urchin, miR-31 knockdown (KD) embryos have shortened dorsoventral connecting rods, mispatterned skeletogenic primary mesenchyme cells (PMCs) and shifted and expanded Vegf3 expression domain. Vegf3 itself does not contain miR-31 binding sites; however, we identified its upstream regulators Eve and Wnt1 to be directly suppressed by miR-31. Removal of miR-31's suppression of Eve and Wnt1 resulted in skeletal and PMC patterning defects, similar to miR-31 KD phenotypes. Additionally, removal of miR-31's suppression of Eve and Wnt1 results in an expansion and anterior shift in expression of Veg1 ectodermal genes, including Vegf3 in the blastulae. This indicates that miR-31 indirectly regulates Vegf3 expression through directly suppressing Eve and Wnt1. Furthermore, removing miR-31 suppression of Eve is sufficient to cause skeletogenic defects, revealing a novel regulatory role of Eve in skeletogenesis and PMC patterning. Overall, this study provides a proposed molecular mechanism of miR-31's regulation of skeletogenesis and PMC patterning through its cross-regulation of a Wnt signaling ligand and a transcription factor of the endodermal and ectodermal gene regulatory network.

Keywords: Even-skipped; MicroRNA-31; Post-transcriptional regulation; Primary mesenchyme cells; Sea urchin; Vegf signaling; Wnt; miRNA target protector.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Animals, Genetically Modified
  • Body Patterning / genetics
  • Embryonic Development / genetics
  • Female
  • Gene Expression Regulation, Developmental*
  • Gene Knockdown Techniques
  • Gene Regulatory Networks
  • Homeodomain Proteins / metabolism*
  • Male
  • Mesenchymal Stem Cells / metabolism
  • MicroRNAs / genetics
  • MicroRNAs / metabolism*
  • Musculoskeletal Development / genetics*
  • Phenotype
  • Signal Transduction / genetics
  • Strongylocentrotus purpuratus / embryology*
  • Strongylocentrotus purpuratus / genetics*
  • Strongylocentrotus purpuratus / metabolism
  • Transcription Factors / metabolism
  • Wnt1 Protein / metabolism*


  • Homeodomain Proteins
  • MicroRNAs
  • Transcription Factors
  • Wnt1 Protein